Double chromodomains cooperate to recognize the methylated histone H3 tail

John F. Flanagan, Li-Zhi Mi, Maksymilian Chruszcz, Marcin Cymborowski, Katrina L. Clines, Youngchang Kim, Wladek Minor, Fraydoon Rastinejad () and Sepideh Khorasanizadeh ()
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John F. Flanagan: Department of Biochemistry and Molecular Genetics
Li-Zhi Mi: Department of Pharmacology
Maksymilian Chruszcz: University of Virginia Health System
Marcin Cymborowski: University of Virginia Health System
Katrina L. Clines: Department of Biochemistry and Molecular Genetics
Youngchang Kim: Argonne National Laboratory, Biosciences Division/Structural Biology Center
Wladek Minor: University of Virginia Health System
Fraydoon Rastinejad: Department of Biochemistry and Molecular Genetics
Sepideh Khorasanizadeh: Department of Biochemistry and Molecular Genetics

Nature, 2005, vol. 438, issue 7071, 1181-1185

Abstract: Abstract Chromodomains are modules implicated in the recognition of lysine-methylated histone tails and nucleic acids1,2. CHD (for chromo-ATPase/helicase-DNA-binding) proteins regulate ATP-dependent nucleosome assembly and mobilization through their conserved double chromodomains and SWI2/SNF2 helicase/ATPase domain3,4,5. The Drosophila CHD1 localizes to the interb ands and puffs of the polytene chromosomes, which are classic sites of transcriptional activity6. Other CHD isoforms (CHD3/4 or Mi-2) are important for nucleosome remodelling in histone deacetylase complexes7,8. Deletion of chromodomains impairs nucleosome binding and remodelling by CHD proteins4. Here we describe the structure of the tandem arrangement of the human CHD1 chromodomains, and its interactions with histone tails. Unlike HP1 and Polycomb proteins that use single chromodomains to bind to their respective methylated histone H3 tails, the two chromodomains of CHD1 cooperate to interact with one methylated H3 tail. We show that the human CHD1 double chromodomains target the lysine 4-methylated histone H3 tail (H3K4me), a hallmark of active chromatin9. Methylammonium recognition involves two aromatic residues, not the three-residue aromatic cage used by chromodomains of HP1 and Polycomb proteins10,11,12,13. Furthermore, unique inserts within chromodomain 1 of CHD1 block the expected site of H3 tail binding seen in HP1 and Polycomb, instead directing H3 binding to a groove at the inter-chromodomain junction.

Date: 2005
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DOI: 10.1038/nature04290

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